The independent counsel investigating the Massachusetts Probation Department has found strong evidence that suspended commissioner John J. O’Brien manipulated his agency’s hiring and promotion process to advance applicants with insider support, according to a source familiar with the investigation.

O’Brien, suspended from his job in May after the Spotlight Team reported that he had hired or promoted at least 250 politically connected job seekers, routinely sent his subordinates lists of his preferred candidates for probation jobs from the Berkshires to Cape Cod, the investigating attorney, Paul F. Ware, has found.

”It’s an immutable fact that this went on,” said the source, who asked not to be named because Ware’s investigation is confidential. Ware has subpoenaed most of O’Brien’s supervisors to learn more about the way people are hired in the 2,200-employee agency.

Meanwhile, the man named to fill O’Brien’s job temporarily has been looking for answers to more basic questions, such as: How many people are on probation in Massachusetts?

”I would say I’m in the process of figuring that out,” said Ronald P. Corbett Jr.

The fact that Corbett, a respected former top probation official, has had to sift for such elemental information underscores the thickness of the curtain behind which O’Brien has operated since 1998.

The Spotlight Team reported yesterday about a culture of secrecy and a disturbing pattern of exaggerated claims and dubious data that raise serious questions about the priorities and competence of the department’s management.

Corbett has ordered sweeping reviews into how the probation agency does its job from determining which probationers are most likely to commit more crimes to the manner in which candidates for top jobs are selected. His moves so far suggest that he wants the department to take a more scientific and transparent approach than O’Brien.

The acting probation administrator is also examining one of O’Brien’s most prized initiatives, the network of 25 Community Corrections Centers that provide drug treatment and education to more than 4,000 offenders a year. The Globe reported yesterday that for years, probation officials failed to examine the effectiveness of the $19.5 million program. The centers’ enrollment has been declining as many public safety officials concluded their programming is lackluster and sometimes useless.

”This is a difficult time, and an unsettling time, and there’s no way around that,” Corbett said. “And the best way to get through it is to keep your head down and do the work in front of you.”

As Corbett works to stabilize an agency rocked by O’Brien’s suspension, Ware, a senior Boston trial counsel whose broad experience in investigating alleged public corruption includes work in the Iran-Contra investigation, is collecting evidence, trying to determine whether laws have been broken.

The Spotlight Team found that, under O’Brien, the agency hired scores of friends and relatives of O’Brien’s inner circle, including his daughter, the daughter of his deputy commissioner, and the nephew of the judge who appointed O’Brien as commissioner. The agency also hired family members of top politicians, including the son of former Boston mayor Raymond L. Flynn, the godson of Massachusetts House Speaker Robert A. DeLeo, and the wife of a top DeLeo deputy, Representative Thomas M. Petrolati.

O’Brien, in an interview with the Spotlight Team before his suspension, denied any favoritism in probation hiring decisions, insisting that the department has an open and elaborate process intended to hire “the appropriate candidate, not just for probation in general, but for the particular court.”

But the source familiar with Ware’s investigation said his investigators already know that O’Brien was heavily involved in hiring decisions from the very beginning. That conclusion was based, in part, on an interview with the Probation Department’s human resources specialist, Janet Mucci, according to the source familiar with the investigation.

It’s not illegal for relatives of politicians and probation officials to hold jobs in the Probation Department, but, if probation managers systematically steered jobs to less-qualified but politically connected candidates, it could violate state conflict of interest law, according to several legal experts. In addition, state law and Massachusetts court policy prohibits the direct hiring of either a blood relative or the blood relative of a spouse.

”Little undercuts the public trust in government more than patronage,” said Pam Wilmot, executive director of Common Cause, a public advocacy group.

O’Brien declined a request to be interviewed for this story. He has retained Milton-based attorney Paul K. Flavin, who said he expects Ware will question his client. “It would be beyond my imagination that he would not seek testimony from Commissioner O’Brien,” Flavin said. O’Brien hopes to address “misconceptions that appeared” in the Globe stories about him during the course of Ware’s inquiry, Flavin said.

The independent counsel is also looking into several cases in which politically connected probation employees appeared to escape serious punishment for major breaches, such as the former associate probation officer in Worcester Superior Court who police say may have compromised an investigation by leaking information to criminals.

Deputy Police Chief Edward J. McGinn Jr. of Worcester said he and two department detectives have been interviewed by Ware about the case of Ashley Losapio, the stepdaughter of a judge, who was transferred to Westborough District Court after McGinn complained about her alleged misconduct and called for a Probation Department investigation.

McGinn wrote a letter to O’Brien in 2008 after Losapio, according to police, admitted hanging around with “bad guys,” had the telephone numbers of criminal suspects programmed into her cellphone, and acknowledged that she would tell those suspects about whom she saw in court. McGinn said O’Brien never contacted him. Losapio kept her job and got a pay increase.

The source familiar with Ware’s investigation said Ware and colleagues at his law firm, Goodwin Procter, are studying campaign contributions by Probation Department employees to see whether there are signs of a “pay to play” system where probation employees were expected to contribute money to certain politicians to improve their chances of promotion. The Spotlight Team in May found a pattern of donations by probation employees to key legislators such as DeLeo and Petrolati just before or after they received promotions.

Ware’s investigation remains “broad ranging,” the source said, but Ware hopes to file an initial report on his findings with the Supreme Judicial Court around Labor Day. The state’s top court gave him until Aug. 22 to complete his work, though some probation observers expect Ware to request an extension.

The SJC has ordered all Probation Department employees to preserve all records created since 2001, including all computer documents, handwritten notes, voicemails, text messages, diaries, calendars, and journal entries.

”No records or documents shall be altered, edited, amended, or destroyed for any reason whatsoever,” the SJC’s order reads.

Corbett was considered the leading choice for the commissioner’s post in late 1997 when O’Brien was appointed to succeed Donald Cochran. Corbett was a deputy commissioner under Cochran. A Harvard graduate, he is a former president of the National Association of Probation Executives, a former editor of a national journal on probation, and was once named the national association’s probation executive of the year. He is now executive director of the SJC.

He said his job now is to calm nerves, steady the ship, and make sure the Probation Department’s basic tasks get carried out.

”People feel that they’re under a cloud, that the profession they’ve committed to has taken a serious hit, and they can’t but feel that personally,” Corbett said during an interview in a conference room at the SJC offices in Pemberton Square.

Corbett said he has been taking time to answer questions during group sessions with chief probation officers and more intimate gatherings with employees across the state. He told employees to try to keep their spirits up, to do their work, and as much as possible to steer clear of the “rumor mill” that roars inside the agency these days.

”Some folks get the sense that maybe - as difficult as this period will be - something good will come from it,” he said.

Corbett said he has already determined that the agency under O’Brien was doing some basic things wrong. For example, he said, the method that O’Brien has used since 1999 to measure the probation agency’s workload is misleading. O’Brien claimed a caseload of 258,667 last year.

”I don’t think that’s the right number to use,” Corbett said in his first interview since he was named acting probation administrator by his judicial superiors.

In 1998, probation officials reported they had 61,621 people under supervision. A year later that number more than doubled, to 157,977, when O’Brien quietly employed new caseload calculations to include every person who rotated in and out of probation over the course of a year, instead of a snapshot of those on probation at any one time.

The real workload number is 92,000, Corbett told the Globe.

Corbett was named to his SJC post in 2000 after a lengthy career in probation. He said he is keeping that job while filling O’Brien’s post on an interim basis. And he said it did not take him long to reacquaint himself with his old agency.

He said he has also made it an early goal to undo the reputation the department acquired under O’Brien for holding itself apart from other public safety agencies, and revealing little about its operations.

”I’ve heard these charges of isolation and insulation,” he said. “What I can do and what I am doing is reaching out to people and telling them now that this is an agency that wants to be at the table.”

Asked whether he wants the probation commissioner’s job that he first sought in the winter of 1997, Corbett demurred.

”I’m not giving that a moment’s thought,” he said. “It would be presumptuous in the extreme, it seems to me, to even reflect on it. So I’m not going to do that. My mandate is to do the best I can during this interim period.”

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